tbuckley/cabot-search huggingface dataset:
Abstract 2566: Blocking the functional domain of TIP1 upregulates midkine via the β-catenin/Wnt signaling pathway
Authors: Minakshi Saikia, Abhay K. Singh, Nathan Cheung, Dennis E. Hallahan, Vaishali Kapoor
Journal: Cancer Research (2023)

Abstract Non-small cell lung cancer (NSCLC) is the leading cause of cancer-related mortalities world-wide. Targeted therapy has been a growing topic of investigation to improve therapeutic efficacy for NSCLC. A few targeted therapies that exploit aberrant protein expression profiles have been approved for NSCLC. However, marginal improvement in efficacy observed with these therapeutic approaches highlights the need for discovery of additional therapeutic targets. Tax interacting protein 1 (TIP1) is a molecular target that is overexpressed on the surface of various cancers and correlates with poor overall patient survival. The functional domain of TIP1 (PDZ domain) caps the C-terminus of many cellular proteins that regulate cell signaling, cancer development, and progression. We found that antibodies against the PDZ domain of TIP1 induced cytotoxicity of lung cancer cells but not normal cells. A quantitative mass spectrometry-based approach identified a ten-fold increase in Midkine protein expression on blockade of TIP1. Midkine is a heparin-binding growth factor that is involved in cancer progression, therapy resistance, and immune suppression. This study tested the hypothesis that Midkine is upregulated by the anti-PDZ/TIP1 antibody via the β-catenin/Wnt signaling pathway, which subsequently modulates downstream signaling mechanisms. In co-immunoprecipitation studies we found a direct interaction of TIP1 with β-catenin on the cell surface. Anti-TIP1 antibody treatment led to nuclear translocation of β-catenin in NSCLC cells. We used a luciferase based TOPFlash/FOPFlash reporter assay to study the transcriptional activity of the canonical β-catenin/Wnt pathway following TIP1 blockade. Reporter assays showed a three to four-fold increase (p&amp;lt;0.0001) in the transcriptional activity of β-catenin following TIP1 blockade in NSCLC cells. Genetic silencing of β-catenin inhibited Midkine mRNA transcription (p&amp;lt;0.005), protein induction and its extracellular release (p&amp;lt;0.0001) following anti-TIP1 antibody treatment. In conclusion, the mechanism of Midkine release following TIP1 blockade involves the β-catenin/Wnt signaling pathway. Ongoing studies are evaluating the dual-targeting of TIP1 and Midkine for enhanced efficacy of NSCLC treatment. Citation Format: Minakshi Saikia, Abhay K. Singh, Nathan Cheung, Dennis E. Hallahan, Vaishali Kapoor. Blocking the functional domain of TIP1 upregulates midkine via the β-catenin/Wnt signaling pathway [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2566.
Abstract 3409: Design and characterization of highly potent and selective CDK9 heterobifunctional degraders
Authors: Mohammed A. Toure, Keisuke Motoyama, André Richters, Angela N. Koehler
Journal: Cancer Research (2023)

Abstract Cyclin-dependent kinase 9 (CDK9) has long been considered an attractive therapeutic target for modulating transcription in cancers of high unmet clinical need. CDK9 coordinates signaling events that regulate RNA polymerase II (Pol II) pause-release state and is considered an important co-factor for oncogenic transcription factors that drive transcription in an addictive manner. CDK9 modulation offers an approach for attenuating transcriptional dysregulation driven by amplified or overexpressed transcription factors, such as c-MYC. However, targeting CDK9 in the clinic has proven very challenging. This stems from the often highly intolerable cytotoxic effects likely due to off-target effects. Targeted protein degradation offers a novel approach for engineering enhanced selectivity and mitigating other liabilities of the conventional inhibition-driven approach that have been applied to date. Here, we present the design and characterization of a focused library of highly selective CDK9 degrader molecules with rapid kinetics and potency (half-degrading concentration of &amp;lt;1nM). We carry out transcriptional and phosphoproteomics profiling to comprehensively characterize the downstream effects and cellular adaptations resulting from CDK9 degradation. We gain new insights into adaptive responses to CDK9 modulation and the biological contexts most responsive for therapeutic application. Citation Format: Mohammed A. Toure, Keisuke Motoyama, André Richters, Angela N. Koehler. Design and characterization of highly potent and selective CDK9 heterobifunctional degraders [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3409.
Abstract 5410: Predictive biomarker discovery method to bridge the gap between preclinical disease model dose-response and clinical trials
Authors: David Futorian, Oren Fischman, Gali Arad, Nitzan Simchi, Omri Erez, Eran Seger, Rozanne Groen, Kirill Pevzner
Journal: Cancer Research (2023)

Abstract The translational gap of drug and biomarker discovery remains one of the biggest challenges in the pharmaceutical industry. On one hand high throughput screening and omics methods facilitate the generation of in-vitro and in-vivo data of dose-response for a particular drug or combinations. On the other hand, clinical omics techniques allow for the creation of large scale treatment-naive clinical datasets, with the TCGA and CPTAC as prominent examples. However, the question of which disease model best represents the response/resistance mechanisms of an oncology patient remains challenging. In this study we present a machine learning (ML) based computational technique for integrating omics from preclinical dose-response studies with clinical treatment-naive samples to create putative predictive biomarkers, and exemplify its application 2 case studies - PARP or AKT inhibitors. We utilize the Cancer Cell Line Encyclopedia (CCLE) and Genomics of Drug Sensitivity in Cancer (GDSC) as a resource for in-vitro dose response data for PARPi and AKTi, coupled with multi-omic molecular data. We utilize the treatment naive molecular characterization from the Clinical Proteomic Tumor Analysis Consortium (CPTAC) data of Breast cancer patients. Multi-omic analysis of these datasets derived 2 putative predictive biomarkers for PARPi and AKTi. The multi-omic analysis resembles the data availability at the critical drug development stage of transition from preclinical response models to a clinical trial. These biomarkers are tested on a validation dataset obtained from the iSPY adaptive clinical trial and achieve superior results compared to the original enrolment biomarkers and even the retrospectively derived biomarkers. This study presents a novel computational approach to bridge the gap between preclinical dose-response and clinical datasets and suggests an efficient way to discover predictive biomarkers based on data accessible in a preclinical setting. Citation Format: David Futorian, Oren Fischman, Gali Arad, Nitzan Simchi, Omri Erez, Eran Seger, Rozanne Groen, Kirill Pevzner. Predictive biomarker discovery method to bridge the gap between preclinical disease model dose-response and clinical trials. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5410.
Abstract 3254: Combination of palbociclib, a potent CDK4/6 inhibitor, with anti-PD1 drug pembrolizumab treatment to promote T-cell mediated glioblastoma tumor cell death under hypoxia
Authors: Yutong Xia, Lanlan Zhou, Shuai Zhao, Wafik S. El-Deiry
Journal: Cancer Research (2023)

Abstract Glioblastoma (GBM) is the most common malignant brain and other central nervous system (CNS) tumor, which comprises 47.7% of all cases. The standard treatment options are surgery, radiation therapy, and chemotherapy using temozolomide. GBM is fast-growing, aggressive, and results in poor overall survival, approximately 40% in the first year and 17% in the second year. Hypoxia, the lack of sufficient oxygen in tissues, is the hallmark of GBM and can induce drug resistance and inhibit anti-tumor immune responses. Previous studies show that CDK inhibitors can destabilize HIF1, a key regulator of hypoxia induced apoptosis and p53 stabilization. Palbociclib, a potent oral inhibitor of CD4/6, is undergoing clinical trials for GBM treatment. However, it was not an effective treatment for recurrent GBM when used as alone in a Phase II study. Thus, we are exploring the cytotoxicity of palbociclib in combination with an anti-PD1 drug pembrolizumab, which is proven to be highly effective in other cancer types. Preliminary studies use CellTitlerGLO viability assay to determine the IC50s for Palbociclib at 24, 48, and 72 hours in both normoxia and hypoxia conditions. Immune cell co-culture, comprising of GBM cell lines plus TALL104 human leukemia T cells, was used to determine the amount of tumor cell death with palbociclib, pembrolizumab and a combination at different time points in both normoxia and hypoxia conditions. Our results are providing insights into improving immune checkpoint therapy for GBM patients. Citation Format: Yutong Xia, Lanlan Zhou, Shuai Zhao, Wafik S. El-Deiry. Combination of palbociclib, a potent CDK4/6 inhibitor, with anti-PD1 drug pembrolizumab treatment to promote T-cell mediated glioblastoma tumor cell death under hypoxia [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3254.
Abstract 4293: Strategies and resources for applying a quantitative multiplex IHC imaging workflow to characterize immune contexture in solid tumors
Authors: Shamilene Sivagnanam, Courtney M. Betts, Nell Kirchberger, Konjit Betre, Lisa M. Coussens
Journal: Cancer Research (2023)

Abstract Conventional immunohistochemistry (IHC) is a standardized diagnostic technique used in tissue pathology. However, the capacity to label only one marker per tissue section is a critical limitation. Multiplex immunohistochemistry (mIHC) is a powerful imaging technique used in basic, translational research and clinical settings to simultaneously detect the expression of multiple epitopes in a single formalin-fixed paraffin-embedded (FFPE) tissue section, allowing for characterization and quantification of cells while maintaining their spatial location. This technique allows for a comprehensive view of the immune milieu, expression patterns, and interactions between cell types that can help elucidate the complexity of the tumor-immune microenvironment (TiME). Multiplex imaging has emerged as a powerful tool to better understand tumor progression, response or resistance to therapy, and potentially identify predictive biomarkers. However, this technique requires careful tissue considerations and generates enormous amounts of hierarchical data, including single cell marker expressions, locations, and shape features, resulting in complex and challenging analyses. We previously published a validated platform using nine matched primary and recurrent head and neck squamous cell carcinoma (HNSCC) sections stained sequentially with a panel of 29 antibodies identifying malignant tumor cells, and 17 distinct leukocyte lineages and their functional states1. Here, we have optimized and consolidated important considerations, including tissue quality and QC steps necessary for generating high quality data from multiplex imaging studies. We demonstrate strategies for a streamline analytic pipeline using our quantitative workflow developed to characterize immune cells and infiltration patterns within spatial compartments of solid tumors in FFPE tissues, and herein, provide strategies and resources to practically adapt and utilize our analytic mIHC pipeline. 1. Banik, G., et al., Methods Enzymol., 2020 Citation Format: Shamilene Sivagnanam, Courtney M. Betts, Nell Kirchberger, Konjit Betre, Lisa M. Coussens. Strategies and resources for applying a quantitative multiplex IHC imaging workflow to characterize immune contexture in solid tumors. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4293.
Abstract 4733: Effect of KDM6A mutation in bladder cancer
Authors: Ninh B. Le, Hong Qiu, Emily E. Fink, Surbhi Sona, Angela H. Ting, Byron H. Lee
Journal: Cancer Research (2023)

Abstract As of 2020, bladder cancer is the tenth most common cancer in the world, with a heavier toll exerted on males. Its higher tumor recurrence and progression rates cause major treatment challenges. One of the most frequent mutations in bladder cancer is in lysine-specific demethylase 6A (KDM6A). This gene encodes for ubiquitously transcribed tetratricopeptide repeat on chromosome X (UTX), which catalyzes the demethylation of di- and tri- methylated histones H3 lysine 27 and works as part of “COMPASS-LIKE” protein complexes to coordinate many transcriptional processes. The molecular basis for how KDM6A mutations promote carcinogenesis is still under investigation. In this study, we use single-cell RNA sequencing data from bladder cancers with and without KDM6A mutations in both human and mice to examine the effects of KDM6A mutations on the cellular composition and gene expression of tumor and normal bladders. In mice without tumors, KDM6A mutations seem to correlate with enrichment of macrophages in the bladder tissue microenvironment. The opposite is true, however, in the presence of tumors, as there were not only more macrophages but also more dendritic cells in wildtype mice. This pattern was also observed in human, suggesting differences in immune infiltrates in the tumor microenvironment are part of the phenotype of KDM6A mutation. Lastly, KDM6A mutations may also impact urothelial cell states at baseline, as KDM6A KO mouse bladders contain higher proportions of intermediate cell populations compared with their wildtype counterparts. Together, these observations contribute to a better understanding of the role KDM6A plays in bladder cancer. Citation Format: Ninh B. Le, Hong Qiu, Emily E. Fink, Surbhi Sona, Angela H. Ting, Byron H. Lee. Effect of KDM6A mutation in bladder cancer. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4733.
Abstract 4059: Developing an allogeneic iPSC derived macrophage cell therapy for oncology
Authors: Huafeng Wang, May Sumi, Christine Huh, Fereshteh Parviz, Jessica Mastroianni, Jane Healy, Nicole Stevens, Leah Mitchell, Susanne Lang, Dan Kaufman, Robert Hollingsworth, David T. Rodgers
Journal: Cancer Research (2023)

Abstract The full potential of cell therapy has yet to be realized in solid tumor indications and new approaches are urgently required. Macrophages are innate immune cells that can kill tumor cells and orchestrate the anti-tumor immune response. Macrophage cell therapy is an exciting new approach to treat cancer with the aim to harness the powerful activity of macrophages to reignite the immune system. Patient derived macrophages, however, are difficult to genetically engineer and do not proliferate, which makes generating high-quality cells at clinically relevant scales challenging. To address this, we have developed an induced pluripotent stem cell (iPSC) approach to macrophage cell therapy. These cells can be genetically engineered at the iPSC stage and then differentiated into billions of highly functional iPSC derived macrophages (iMACs). This allogenic cell therapy product can then be cryopreserved and stored for immediate use in the clinic when the patient is ready. Here we show that iMACs function like normal macrophages. They migrate towards tumor cells, respond to challenges through innate immune receptors, and produce immune recruiting and activating cytokines and chemokines. iMACs also express high levels of antibody receptors and we show that these cells can be directed to kill tumors in vitro and in vivo via antibody dependent cellular phagocytosis. Furthermore, we have conducted a robust screen to develop a novel CAR that is optimized for use in iMACs. These receptors can be engineered into iMACs at the iPSC stage and trigger robust tumor cell killing. In summary, these data highlight the therapeutic potential of iMACs in oncology and support the further development of this technology for clinical use. Citation Format: Huafeng Wang, May Sumi, Christine Huh, Fereshteh Parviz, Jessica Mastroianni, Jane Healy, Nicole Stevens, Leah Mitchell, Susanne Lang, Dan Kaufman, Robert Hollingsworth, David T. Rodgers. Developing an allogeneic iPSC derived macrophage cell therapy for oncology. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4059.
Abstract 3875: Evaluation of resistance mechanisms to ARV471, an ER-targeted PROTAC
Authors: Delia Margaret Friel, Zachary Sandusky, Yijia Jiang, Xintao Qiu, Rong Li, Henry Long, Rinath Jeselsohn, Myles Brown
Journal: Cancer Research (2023)

Abstract Estrogen receptor alpha (ER) is a ligand activated transcription factor and a driver of ER+ breast cancer. The discovery of activating mutations in ER (gene name ESR1), in patients with advanced endocrine-resistant ER+ breast cancer, has ignited a large pharmaceutical effort to develop next-generation ER antagonists that also target the mutant protein. Here, we profiled the potency and selectivity of many next-generation ER antagonists currently in clinical trials, including ER-targeted proteolysis-targeting chimeras (PROTACs), selective ER modulators (SERMs), and selective ER degraders (SERDs). To contextualize these antagonists, we evaluated their activity against the only FDA-approved SERD, Fulvestrant, at the level of chromatin, transcriptome, proteome, and cell viability, using cells expressing wild-type ER as well as activating mutant ER (ERY537S and ERD538G). Overall, we find that many of the novel oral SERDs are potent ER antagonists, including against mutant ER. To anticipate resistance mechanisms to these next-generation ER antagonists, we developed a strategy initially focused on ARV471 (the most clinically advanced ER PROTAC), with two approaches. First, we performed whole-genome CRISPR/Cas9-knockout screening in ER+ breast cancer cell lines treated with ARV471. Among the enriched gRNAs were PTEN, NF2, and CRBN. Loss of PTEN and NF2 results in activation of the PI3K and MAPK pathways, respectively, and CRBN is the ubiquitin E3 ligase required for ER protein degradation by ARV471. PTEN and NF2 are known mechanisms of endocrine resistance but it is not yet known if CRBN loss in response to PROTACs is a predominant clinical resistance mechanism. Therefore, in a second approach we generated ARV471 resistant breast cancer cell lines through long term exposure (LTE-ARV471). These cells developed an ER-independent resistance mechanism, with decreased ER expression and increased expression of pathways associated with Ras/MAPK and EMT. Therefore, as more potent ER degraders enter the clinic, such as PROTACs and oral SERDs, it may be important to monitor resistance mechanisms that involve loss of ER. Currently, we are following up our findings with LTE-ARV471 cells and performing CRISPR screening to identify targetable dependencies and combination therapies for endocrine resistant breast cancer. Citation Format: Delia Margaret Friel, Zachary Sandusky, Yijia Jiang, Xintao Qiu, Rong Li, Henry Long, Rinath Jeselsohn, Myles Brown. Evaluation of resistance mechanisms to ARV471, an ER-targeted PROTAC. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3875.
Abstract 3971: Developing cancer cell based <i>in vitro</i> and <i>in vivo</i> models with CRISPR-mediated knock-in technology for anti-tumor drug discovery
Authors: Nengwei Xu, Reifeng Wang, Jian Xiang, Qingyang Gu, Xiangnan Qiang
Journal: Cancer Research (2023)

Abstract Human cancer cell lines have long been applied for anti-tumor drug discovery considering their acquired genomic diversity of different carcinomas. Genetic engineering based on cancer cell lines is no doubt a useful and promising approach in induction of new therapeutic targets/elements while maintaining intrinsic characteristics of original cell in parallel. Recently, the emergence of CRISPR knock-in technology has accelerated precise editing across whole genome, from gene depletion, small fragment insertions to site-direct mutations, thereby prompting our understanding of the influence of a specific oncotarget in given tumor genetic background. Herein, by employing CRISPR/Cas9 system, two human cancer cell line-based, inheritable drug resistance models were established where the mutation site C481S of BTK in REC-1 conferred resistance to Ibrutinib and the mutation site R537S/D538G of ESR1 exerted resistance to Fulvestrant in MCF-7. In addition, the engineered cell models also enable the mechanism characterization and development of viable therapeutic agents targeting those oncogenic-driver mutations in a subtype of cancers. The murine colon cancer cell line CT26, which harbors KRASG12D mutation, was genetically modified to express KRASG12C protein to allow for an expandable pocket providing opportunities for compound recruitment. The resultant KRASG12C CT26 cell line showed pronounced inhibitory effect after treatment with AMG510. More interestingly, the therapeutic combination involving both AMG510 and anti-PD1 antibodies demonstrated more effective anti-tumor activities when compared to monotherapy. Moreover, CRIPSR-mediated engineered knock-in cells with a traceable tag linked to endogenous oncotarget also exhibit capability in new therapeutic modality discovery. Based on HiBiT protein tagging technology, we generated a series of HiBiT knock-in cell lines for real-time cell-based protein degradation analysis on various compelling targets, such as ESR1, KRAS, and BRD4, et al. Thereby, the construction of these in vitro and in vivo models with the ease of CRISPR KI technology is indispensable in new generation of therapeutic drug exploration. Citation Format: Nengwei Xu, Reifeng Wang, Jian Xiang, Qingyang Gu, Xiangnan Qiang. Developing cancer cell based in vitro and in vivo models with CRISPR-mediated knock-in technology for anti-tumor drug discovery. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3971.